LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file

# run the first part and write out restart
include in.template-mix
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms

units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
  1 molecules
  0 fragments
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
atom_style template cychex

pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic

lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24 -24 -24) to (24 24 24)
  1 by 1 by 1 MPI processor grid

create_atoms 0 box mol cychex 734594
Created 3072 atoms
  using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
  create_atoms CPU = 0.000 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
  using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
  create_atoms CPU = 0.000 seconds

mass 1 14.027
mass 2 16.043

pair_coeff 1 1  0.1180  3.905
pair_coeff 2 2  0.2940  3.730

bond_coeff      1  260.00 1.5260
angle_coeff     1  63.0   112.40
dihedral_coeff  1  2.0 1 3

thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.05 | 8.05 | 8.05 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0              4.3897851e+13  341.92144      4.3897851e+13  1.0886888e+14
       100   0             -4351.8383      516.49891     -3835.3394      11635.037    
       190   0             -6191.8196      457.61266     -5734.2069      4365.4279    
Loop time of 2.46574 on 1 procs for 190 steps with 3872 atoms

99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
      43897850768892.8  -5729.17409504969  -5734.20694761353
  Force two-norm initial, final = 1.1080994e+15 72.745546
  Force max component initial, final = 4.6607099e+14 17.390179
  Final line search alpha, max atom move = 0.0041638487 0.072410076
  Iterations, force evaluations = 190 297

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.1376     | 2.1376     | 2.1376     |   0.0 | 86.69
Bond    | 0.068456   | 0.068456   | 0.068456   |   0.0 |  2.78
Neigh   | 0.21212    | 0.21212    | 0.21212    |   0.0 |  8.60
Comm    | 0.012436   | 0.012436   | 0.012436   |   0.0 |  0.50
Output  | 2.9907e-05 | 2.9907e-05 | 2.9907e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.03511    |            |       |  1.42

Nlocal:           3872 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          12122 ave       12122 max       12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         774375 ave      774375 max      774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0

velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   100           -6191.8196      457.61266     -4580.3354      4842.371     
       100   106.81292     -5670.2785      921.2043      -3516.5903      5959.4321    
       200   119.24063     -5701.0127      1040.0231     -3285.1059      6755.2619    
       300   127.28216     -5706.3887      1026.2838     -3211.4322      6076.6123    
       400   133.79038     -5734.0279      1113.6088     -3076.65        6583.9393    
       500   138.77685     -5756.2532      1192.1349     -2962.8117      6436.3524    
       600   149.39857     -5730.563       1206.6372     -2800.0582      6357.5889    
       700   155.5825      -5671.0161      929.50406     -2946.2899      7697.5164    
       800   161.24677     -5628.3833      1186.5533     -2581.2493      5840.6503    
       900   172.81747     -5638.6453      1148.683      -2495.8707      8169.3352    
      1000   182.2048      -5579.5767      909.90783     -2567.2594      6270.7354    
      1100   188.95766     -5548.999       1183.6644     -2185.0058      7711.9244    
      1200   195.22147     -5511.6798      1111.3361     -2147.7386      7656.4439    
      1300   205.15867     -5431.6966      1195.8143     -1868.6148      7021.8716    
      1400   211.44641     -5410.5687      1299.0501     -1671.6986      8903.0061    
      1500   223.70124     -5359.4567      1388.4189     -1389.8128      6919.2408    
      1600   231.75318     -5288.3343      1348.829      -1265.3712      9409.2728    
      1700   229.61746     -5259.4318      1194.5663     -1415.375       7387.4923    
      1800   245.62483     -5281.0755      1389.3362     -1057.5441      9421.7241    
      1900   250.69445     -5158.7006      1236.5167     -1029.4919      8649.4835    
      2000   259.50657     -5148.4153      1485.1392     -668.90355      9130.4701    
      2100   270.77108     -5092.6634      1418.7937     -549.51913      9666.5632    
      2200   272.30152     -5079.7585      1514.5708     -423.17779      8568.2546    
      2300   285.20945     -5085.6197      1492.5671     -302.10191      10281.574    
      2400   286.95799     -4979.8608      1544.6159     -124.11819      8797.7435    
      2500   296.10218     -4928.5152      1698.282       186.40572      10946.864    
Loop time of 16.1773 on 1 procs for 2500 steps with 3872 atoms

Performance: 13.352 ns/day, 1.797 hours/ns, 154.537 timesteps/s, 598.368 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 14.927     | 14.927     | 14.927     |   0.0 | 92.27
Bond    | 0.52161    | 0.52161    | 0.52161    |   0.0 |  3.22
Neigh   | 0.52299    | 0.52299    | 0.52299    |   0.0 |  3.23
Comm    | 0.090871   | 0.090871   | 0.090871   |   0.0 |  0.56
Output  | 0.00059782 | 0.00059782 | 0.00059782 |   0.0 |  0.00
Modify  | 0.096104   | 0.096104   | 0.096104   |   0.0 |  0.59
Other   |            | 0.01791    |            |       |  0.11

Nlocal:           3872 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11821 ave       11821 max       11821 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         770416 ave      770416 max      770416 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 770416
Ave neighs/atom = 198.97107
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data template-mix.data
#write_restart template-mix.restart
write_restart template-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule

# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
  1 molecules
  0 fragments
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
  restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
  restoring atom style template from restart
  orthogonal box = (-24 -24 -24) to (24 24 24)
  1 by 1 by 1 MPI processor grid
  restoring pair style lj/cut from restart
  restoring bond style harmonic from restart
  restoring angle style harmonic from restart
  restoring dihedral style harmonic from restart
  3872 atoms
  3072 template bonds
  3072 template angles
  3072 template dihedrals
  read_restart CPU = 0.001 seconds

thermo 100

fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
  fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      2500   296.10218     -4928.5152      1698.282       186.40572      10946.864    
      2600   302.98473     -4910.6997      1585.9276      171.28257      9066.357     
      2700   300.75989     -4935.1005      1723.6514      258.9337       10755.67     
      2800   294.26086     -4904.3072      1594.9394      86.02469       9420.9997    
      2900   296.15059     -4961.5041      1594.1004      49.793724      10129.823    
      3000   296.65334     -4934.6622      1596.9704      85.306731      10112.636    
      3100   301.62361     -4975.5261      1671.8512      176.67422      9500.7576    
      3200   297.34385     -5017.986       1603.4388      16.419054      10451.2      
      3300   297.01108     -4882.1137      1651.6426      196.65525      9124.096     
      3400   298.13642     -4983.4532      1742.3589      199.01715      10808.599    
      3500   315.91146     -4952.209       1651.2231      344.22669      8677.2632    
      3600   295.12433     -4950.6158      1721.3273      176.06725      10904.222    
      3700   300.65909     -4967.4001      1770.4243      272.244        9230.4292    
      3800   302.15034     -4991.9549      1644.8366      139.30847      10154.524    
      3900   302.16277     -5017.0117      1672.2353      141.79397      9705.6697    
      4000   303.1458      -4946.2517      1679.8498      231.51137      9527.8793    
      4100   303.54737     -5003.8276      1639.7221      138.44129      10406.442    
      4200   291.62491     -5009.3438      1707.6         63.233087      8645.4116    
      4300   306.17115     -5084.7139      1727.9528      176.0607       10563.216    
      4400   302.65581     -5004.4302      1747.5309      235.36003      8717.1253    
      4500   296.42334     -5014.9791      1723.2084      128.57389      10492.246    
Loop time of 13.2399 on 1 procs for 2000 steps with 3872 atoms

Performance: 13.051 ns/day, 1.839 hours/ns, 151.058 timesteps/s, 584.898 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 12.13      | 12.13      | 12.13      |   0.0 | 91.61
Bond    | 0.42044    | 0.42044    | 0.42044    |   0.0 |  3.18
Neigh   | 0.52469    | 0.52469    | 0.52469    |   0.0 |  3.96
Comm    | 0.072857   | 0.072857   | 0.072857   |   0.0 |  0.55
Output  | 0.00053188 | 0.00053188 | 0.00053188 |   0.0 |  0.00
Modify  | 0.076918   | 0.076918   | 0.076918   |   0.0 |  0.58
Other   |            | 0.0148     |            |       |  0.11

Nlocal:           3872 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11685 ave       11685 max       11685 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         770346 ave      770346 max      770346 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 770346
Ave neighs/atom = 198.953
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0

# clean up
shell rm template-mix.restart
Total wall time: 0:00:31
